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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
my $usage = "usage: $0 fasta_file\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $fasta_reader = new Fasta_reader($fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
my $contig_acc = $acc;
$acc =~ s/;/_/;
my $seq = $seq_obj->get_sequence();
my $seq_len = length($seq);
print join("\t", $contig_acc, ".", "transcript", 1, $seq_len, ".", "+", ".",
"gene_id \"g.$acc\"; transcript_id \"t.$acc\";") . "\n";
print join("\t", $contig_acc, ".", "exon", 1, $seq_len, ".", "+", ".",
"gene_id \"g.$acc\"; transcript_id \"t.$acc\";") . "\n";
print "\n";
}
exit(0);
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